On Sun, Aug 23, 2009 at 10:30 AM, Jamie Seyed <jamie.se...@gmail.com> wrote:
> Hi Justin, > Thanks for the answers. Please check below... > > On Sat, Aug 22, 2009 at 9:17 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > >>> >>> On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >>> jalem...@vt.edu>> wrote: >>> >>> >>> >>> Jamie Seyed wrote: >>> >>> Hi Justin and Mark, >>> Thanks. Actually I made a mistake and it seems going to the zero >>> (even negative!) >>> --But I wanted to know how I can write my command to get only >>> one graph (average of all instead of all of them). I read the >>> manual chapter-8 and by average I mean I should get one curve >>> starting at 1 and coming down to zero...I also tried >>> >>> >>> That's not an average; that's the shape of the ACF curve. >>> >>> Yes I need to get that shape using g_analyze..!. >>> >> >> Right, I just don't understand why you think you need to obtain some sort >> of average. What do you mean by "all of them"? How many graphs are there? > > > Actually when I open autocorr.xvg I can see from data/feature extraction/ > the last set is S1295 (N=101, autocorr.xvg) which means they are 1296 > graphs each with poor statistics start at 1 and coming down. To have a ACF > for a system I expect to get one graph with good statistic... I hope I make > it clear now. > >> >> >> <snip> >> >> No, only ACF based on coordinates. I read from the list that people said I >>> can use g_rotacf -d for calculation of correlation functions...and actually >>> I did it for a simple system. But for new system using another index file it >>> is complaining. >>> >>> >> Then I don't think g_rotacf is the tool you want. There is no magic way >> to simply calculate some sort of general correlation function. You >> calculate an ACF from the specific data you have. So if you're interested >> in some sort of position-dependent data, then rotational properties may or >> may not be relevant. >> >> You can certainly use g_rotacf if you think it will be meaningful; see >> below regarding your .tpr file. >> >> <snip> >> >> tpbconv -s f.tpr -f f.trr -n f.ndx -o tpxout.tpr >>> >>> >> >> Don't use -f. If you do, tpbconv will think you are trying to create a >> new .tpr file that starts off from the time frame present in the .trr file. > > > Yes I removed -f and I got tpxout.tpr and used it for g_rotacf > g_rotacf -f f.xtc -s tpxout.tpr -n f.ndx -o rotacf.xvg -d > but the result I got is like y=2x that starts at (0,0) which y=C(t) and > x(Time,ps). Which is very strange... I don't understand what are these > results using this command. (I should mention that f.xtc contains the > coordinates of selected atoms). Many thanks for your attention and your > help/Jamie > Please ignore this part since I used wrong files.../Thanks, Jamie > > >> >> -Justin >> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
